feat: add pairwise distance computation and phylogenetic trees

This commit introduces a new `distance` CLI subcommand that computes pairwise genomic distance matrices using configurable metrics (Jaccard, Hamming, Bray-Curtis, Euclidean, and Hellinger). It optionally generates phylogenetic trees (NJ or UPGMA) in Newick format and outputs results as CSV. The implementation adds a robust distance computation backend that dynamically routes to optimized backends based on index configuration, supports parallel iteration, and gracefully handles missing data. Additionally, it adds a `dump` task for exporting k-mer to genome mappings as CSV, introduces an `InvalidInput` error variant, updates dependencies to support numerical operations and tree construction, and performs minor module reorganizations.

src/obikpartitionner/src/distance.rs

@@ -0,0 +1,47 @@
+use obicompactvec::{PersistentBitMatrix, PersistentCompactIntMatrix};
+use obilayeredmap::LayeredStore;
+use obiskio::{SKError, SKResult};
+
+use crate::partition::KmerPartition;
+
+const INDEX_SUBDIR: &str = "index";
+
+fn probe_n_layers(index_dir: &std::path::Path) -> usize {
+    let mut n = 0;
+    while index_dir.join(format!("layer_{n}")).exists() { n += 1; }
+    n
+}
+
+impl KmerPartition {
+    /// Open all count matrices for partition `part`, one per layer.
+    /// Layers without a `counts/` directory are skipped.
+    pub fn count_store(&self, part: usize) -> SKResult<LayeredStore<PersistentCompactIntMatrix>> {
+        let index_dir = self.part_dir(part).join(INDEX_SUBDIR);
+        if !index_dir.exists() {
+            return Ok(LayeredStore::new(vec![]));
+        }
+        let matrices = (0..probe_n_layers(&index_dir))
+            .filter_map(|l| {
+                let dir = index_dir.join(format!("layer_{l}")).join("counts");
+                dir.exists().then(|| PersistentCompactIntMatrix::open(&dir).map_err(SKError::Io))
+            })
+            .collect::<SKResult<Vec<_>>>()?;
+        Ok(LayeredStore::new(matrices))
+    }
+
+    /// Open all presence matrices for partition `part`, one per layer.
+    /// Layers without a `presence/` directory are skipped.
+    pub fn presence_store(&self, part: usize) -> SKResult<LayeredStore<PersistentBitMatrix>> {
+        let index_dir = self.part_dir(part).join(INDEX_SUBDIR);
+        if !index_dir.exists() {
+            return Ok(LayeredStore::new(vec![]));
+        }
+        let matrices = (0..probe_n_layers(&index_dir))
+            .filter_map(|l| {
+                let dir = index_dir.join(format!("layer_{l}")).join("presence");
+                dir.exists().then(|| PersistentBitMatrix::open(&dir).map_err(SKError::Io))
+            })
+            .collect::<SKResult<Vec<_>>>()?;
+        Ok(LayeredStore::new(matrices))
+    }
+}

src/obikpartitionner/src/lib.rs

@@ -1,3 +1,4 @@
+mod distance;
 mod dump_layer;
 mod index_layer;
 mod kmer_sort;